Dear community members,
I got a CRAM aligned to a very customised reference with weird (not even "canonical" alt) contigs. They are not covered except several accidental reads and I can safely filter them out. Is there a way to do it for CRAM (I don't have this custom reference)? I know how to do it with BAM, but not sure if it will work with CRAM...
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German.M.Demidov
Perhaps you can create a dummy reference containing N's for the weird contigs (while matching the lengths).
Then use the valid sequences for the contigs you want to keep - if I read it correctly you have the main contigs - only the weird-ALTs are missing
then use that dummy reference to filter the CRAM file by the desired contigs.
this answer is the essence of bioinformatics - I am sure it will work but wow...
indeed bioinformatics is more about how to work around the endless foundational problems or as Brent Pedersen put it 10 years ago:
I've been doing bioinformatics for about 10 years now. I used to joke with a friend of mine that most of our work was converting between file formats. We don't joke about that anymore.
10+10, makes the sentiment 20 year old now, and still applies just as much
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I'm not sure you can do much things with a CRAM without reference...